From 92f577319f64a55dec3d7563d5f15569658ac0de Mon Sep 17 00:00:00 2001 From: Sanjay Kumar Srikakulam Date: Thu, 28 Nov 2024 17:04:26 +0000 Subject: [PATCH] add HDF5_USE_FILE_LOCKING ENV and set it to false in TPV tool defaults --- files/galaxy/tpv/tool_defaults.yml | 5 ++++- files/galaxy/tpv/tools.yml | 5 ----- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/files/galaxy/tpv/tool_defaults.yml b/files/galaxy/tpv/tool_defaults.yml index 19d3d0b3c..655d5cf59 100644 --- a/files/galaxy/tpv/tool_defaults.yml +++ b/files/galaxy/tpv/tool_defaults.yml @@ -8,7 +8,10 @@ tools: mem: cores * 3.8 gpus: 0 env: - GALAXY_MEMORY_MB: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952 + - name: GALAXY_MEMORY_MB + value: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952 + - name: HDF5_USE_FILE_LOCKING + value: "FALSE" params: metadata_strategy: "extended" tmp_dir: true diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 1b7dc98dd..12a171e67 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -207,11 +207,6 @@ tools: prefer: - condor-tpv - toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*: - env: - - name: HDF5_USE_FILE_LOCKING - value: "FALSE" - toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*: rules: - if: input_size >= 0.01